Interact with the puddle, and use the bucket with the poisoned water when the inventory window appears. There will be an option to empty the bucket.
Note: Not 100% sure, but i think the puddle need to be poisoned to empty the poisoned water bucket. In the same way the puddle need to be clean to empty the non poisoned water bucket.
You can use that purifying machine thing to alternate the puddle between poisoned/not poisoned, using the herbicide poison again for the later.